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NM_001165963.4(SCN1A):c.5876T>C (p.Met1959Thr) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Sep 1, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002275856.11

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5876T>C (p.Met1959Thr)]

NM_001165963.4(SCN1A):c.5876T>C (p.Met1959Thr)

Genes:
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.5876T>C (p.Met1959Thr)
HGVS:
  • NC_000002.12:g.165991399A>G
  • NG_011906.1:g.87241T>C
  • NM_001165963.4:c.5876T>CMANE SELECT
  • NM_001165964.3:c.5792T>C
  • NM_001202435.3:c.5876T>C
  • NM_001353948.2:c.5876T>C
  • NM_001353949.2:c.5843T>C
  • NM_001353950.2:c.5843T>C
  • NM_001353951.2:c.5843T>C
  • NM_001353952.2:c.5843T>C
  • NM_001353954.2:c.5840T>C
  • NM_001353955.2:c.5840T>C
  • NM_001353957.2:c.5792T>C
  • NM_001353958.2:c.5792T>C
  • NM_001353960.2:c.5789T>C
  • NM_001353961.2:c.3434T>C
  • NM_006920.6:c.5843T>C
  • NP_001159435.1:p.Met1959Thr
  • NP_001159436.1:p.Met1931Thr
  • NP_001189364.1:p.Met1959Thr
  • NP_001340877.1:p.Met1959Thr
  • NP_001340878.1:p.Met1948Thr
  • NP_001340879.1:p.Met1948Thr
  • NP_001340880.1:p.Met1948Thr
  • NP_001340881.1:p.Met1948Thr
  • NP_001340883.1:p.Met1947Thr
  • NP_001340884.1:p.Met1947Thr
  • NP_001340886.1:p.Met1931Thr
  • NP_001340887.1:p.Met1931Thr
  • NP_001340889.1:p.Met1930Thr
  • NP_001340890.1:p.Met1145Thr
  • NP_008851.3:p.Met1948Thr
  • LRG_8:g.87241T>C
  • NC_000002.11:g.166847909A>G
  • NM_001165963.1:c.5876T>C
  • NR_148667.2:n.6293T>C
Protein change:
M1145T
Links:
dbSNP: rs1368302993
NCBI 1000 Genomes Browser:
rs1368302993
Molecular consequence:
  • NM_001165963.4:c.5876T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.5792T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.5876T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.5876T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.5843T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.5843T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.5843T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.5843T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.5840T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.5840T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.5792T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.5792T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.5789T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.3434T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.5843T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.6293T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002562642GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(Feb 11, 2022) 		germlineclinical testing

Citation Link,

SCV004147165CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Uncertain significance
(Sep 1, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV002562642.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This substitution is predicted to be within the C-terminal cytoplasmic domain.; Has not been previously published as pathogenic or benign to our knowledge

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV004147165.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

SCN1A: PM2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2024